Functional Anatomy

Dr Swinney

Lectures 7-8 (18-11-16)



  • Located near the midline of the brain, above the midbrain
  • Contains the thalamic structures: Epithalamus, Thalamus, Hypothalamus
  • The gate keepers of what enters and exits teh cerebellum- highlights the importance of position with the brain
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  • Relay station for all sensory impulses to the cerebral cortex (except smell which is associated with the hypothalamus)
  • Pain, temperature and pressure relayed here en route to higher centers of the cerebral cortex
  • Not precisely localised (cerebral cortex), all peripheral sensations processed in conjunction with the memories they evoke 
  • Regulates what leaves and enters to prevent sensory overload
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  • Below thalamus
  • Collection of neurochemically distinct nuclei
  • Uses hormones and neurochemicals to maintain homeostasis (stable internal environment despite changing external enivironment

Master Gland controls...

  • Autonomic nervous system
  • Coordinates between nervous system and endocrine system
  • Body temperature (measured by blood flowing through)
  • Hunger/ thirst/ satiety
  • Internal cardian clock- superciesmatic nucleus/ body clock
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Brain Stem

  • Superior to but continues with the spinal cord
  • Represents a group of anatomical components: (from top) Midbrain ---> Pons ---> Medulla Oblongata
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Medulla Oblongata

  • Begins at inferior border of the pons an extends to the foramen magnum
  • Contains all ascending and descending tracts extending between the spinal cord and cerebrum
  • Contains nuclei which are regulators for various vital body functions
  • Has two external bulges call the pyramids, formed by the largest motor tracts in the body
  • Axons on the left pyramid cross to the right side and vice versa (desussation of pyramids)- left side of the brain controls the right side of the body

Functional centres

  • Cardiovascular: Rate and force of heartbeat and diameter of blood vessels
  • Respiratory Rhythmicity Centre: Rate and rhythm of breathing
  • Vomiting, Coughing and Sneezing
  • Nuclei associate with 5 of 12 cranial nerves originate here
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  • Directly above medulla, anterior to cerebellum
  • Bridge connecting spinal cord with brain and parts of the brain with eachother
  • Inhalation. exhalation
  • Pontine respiratory group, normally inactive during quiet breathing- group of neurons act as an off switch to terminate medullary inspiratory activity
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  • Extends from pons to diencephalon
  • Cerebral aqueduct passes through midbrain connecting 3rd ventricle above with 4th ventricle below


  • Substantia nigra: Controls subconscious muscle activity, releases dopamine, loss of these neurons is associated with Parkinson's disease
  • Raphe: Releases serotonin
  • Locus coeruleus: Releases noradrenaline
  • Pedunculopontine: Releases acetyl choline
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Reticular Formation

  • Organisation only found in the cerebral cortex
  • Netlike arrangement of neuronal cell bodies and small bundles of myelinated axons in brain stem

Reticular Activating System

  • Ascening portion
  • Consists of sensory acons that project to the cerebral cortex
  • Maintains consciousness
  • Inactivation results in sleep
  • Anasthetics effect this area
  • Prevents sensory overload
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  • Develops very late and is maluble at young age explaining why aquisation of language is easier 
  • 2nd largest part in the brain
  • Inferior to cerebrum, posterior to brainstem
  • Main neuron= Purkinje Neuron
  • Involved in unconscious motor coordination
  • Cognition and emotion
  • Target for alcohol
  • Autism, ataxia
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The Diffuse Modulatory Systems of the Brain


  • Serotonergic Raphe Nuclei
  • Dopaminergic Substatia Nigra Ventral Tegmental Area
  • Noradrenergic Locus Coeruleus
  • Cholinergergic Basal Forebrain and Brain Stem Complexes

Common Principles of Systems

  • Small set of neurons at core
  • Arise from brain stem
  • One neurone influences many others
  • Synapses release transmitter molecules into extracellular fluid
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Serotonin 1

  • Originates from collections of nuclei (the main one being the dorsal raphe) in the raphe (brainstem)
  • Axons innervate almost entire brain to release serotonin, acting on serotonergic receptors
  • Depression, anxiety, sleep disorders, pain
  • One chemical but multiple receptors---> chemical has many different functions

Serotonin Receptor Classes

  • 13 receptors divided into 7 classes which are divided into sub classes
  • All G-protein coupled receptors (GPCRs) apart from 5HT3 which is an ionoprotic receptor
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Serotonin 2

Drugs acting on 5HT receptors

  • Clozapine, Resperidone, Olanzapine: agonists at 5HT2A receptors (D2 receptors), used to treat psychosis
  • Sumatriptan and other triptans: agonists of 5HT1D, used to treat migraines
  • Buspirone, Gepirone: partial agonist at 5HT1A, used to treat generalised anxiety disorder (GAD)
  • Odansetron, Granisetron: agonists of 5HT3, used as antiemetics

Drugs acting on 5HT transporters (SERT)

  • Fenfuramine: reversible transport of 5HT into synapse---> more 5HT in the synapse meaning there is more 5HT to act on receptors, used to treat obesity
  • SSRIs (selective serotonin reuptake inhibitors) e.g. Fluoxetine: block 5HT transporter meaning there is more in the synapse, used to treat depression
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Dopamine 1


  • Ventral tegmental area: motivation, cognition, reward
  • Substantia nigra: voluntary movement
  • Hypothalamus: breast milk

Effect of Dopamine depends on the brain region


  • Parkinson's
  • Schizophrenia
  • Addiction
  • Hormonal disorders
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Dopamine 2


  • 5 receptors, all G protein coupled receptors GRCRs
  • Functionally classified: D1 family (D1 + D5) and D2 family (D2,3,4)
  • Neuronal excitation/ inhibition depends on G proteins they are coupled to


  • L-Dopa: converts to Da when it enters the CNS increasing dopamine levels, used to treat parkinson's
  • Bromocriptine: D2 agonist, sometimes used to treat parkinson's but mainly used in the treatment of hyperprolactineamia (unnecessary production of breast milk)
  • Haloperidol: D2 agonist, used to treat schizophrenia
  • Clozapine: D4 agonist (also blocks 5HT), used to treat schizophrenia)
  • Cocain: inhibits dopamine (and noradrenaline) transporters preventing removal, therefore there is more dopamine in the synapse
  • Amphetamineincreases DA release
  • Modafinil and Methylphenidate (Ritaline): increases DA in the synapse, resulting in increased wakefullness and concentration, used to treat narcolepsy and ADHD
  • MDMA (Ecstasy): increased dopamine, serotonin and noradrenaline
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Noradrenaline 1

  • Main nucleus: locus coeruleus (LC)
  • Axons of LC innervate almost the whole brain to release noradrenaline
  • Focus, attention


  • Impaired conition/ memory---> alzheimers
  • Mood disorders---> depression
  • Attentional disorders---> ADHD


  • Alpha 1 (A,B, D) and 2 (A,B,C)
  • All metabotropic coupled to different G-proteins
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Noradrenaline 2

Na transmission in the CNS:

  • Arousal system 
  • Blood pressure
  • Control of mood
  • Selective noradrenergic reuptake inhibitors (NRIs) inhibit Na transporters meaning there is more in the synapse---> mechanism used by antidepressants e.g. Bupropion, Reboxetine, atomextine
  • Mixed noradrenaline-serotonin reuptake inhibitors (SNRIs) e.g. Venlafaxine, increases serotonin and noradrenaline in the synapse, used to treat depression
  • Psychotic drugs act partly/ mainly on Na transmission in the CNS e.g. Cocaine and Amphetamines
  • ReserpineVMAT inhibitor, depreting Na in synaptic vesicles resulting in less Na being released into the synapse, can induce depression
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Acetyl choline


  • Basal nucleus
  • Medial spetal nucleus and diagnonal band

send axons to the cortex causing arousal, emotion and cognition

  • Penduculopontine nucleus- located in the brainstem

send axons to dopamine neurones of VTA, important for reward


  • Depression
  • Impaired cognition and memory: Alzheimer's
  • Motor coordination
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